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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iSEEu.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iSEEu_1.10.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/iSEEu.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iSEEu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iSEEu’ version ‘1.10.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘iSEEu’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘iSEEhex’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘iSEE:::.dataParamBoxOpen’ ‘iSEE:::.multiSelectHistory’
  ‘iSEE:::.noSelection’ ‘iSEE:::.organizationHeight’
  ‘iSEE:::.organizationWidth’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: '.setOrganism' is deprecated.
  Warning: '.setIdentifierType' is deprecated.
  Warning: 'GeneSetTable' is deprecated.
  Warning: 'setPValuePattern' is deprecated.
  Warning: 'setPValuePattern' is deprecated.
  Warning: '.setIdentifierType' is deprecated.
  Warning: '.getIdentifierType' is deprecated.
  Warning: '.setOrganism' is deprecated.
  Warning: '.getOrganism' is deprecated.
  Warning: '.getGeneSetCommands' is deprecated.
  Warning: '.getOrganism' is deprecated.
  Warning: '.getOrganism' is deprecated.
  Warning: '.getGeneSetCommands' is deprecated.
  Warning: '.getIdentifierType' is deprecated.
  Warning: '.getOrganism' is deprecated.
  Warning: '.getOrganism' is deprecated.
  Warning: '.setGeneSetCommands' is deprecated.
  Warning: '.getGeneSetCommands' is deprecated.
  Warning: '.getGeneSetCommands' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
AggregatedDotPlot                 15.311  1.513  17.388
modeReducedDim                    12.468  0.432  13.342
FeatureSetTable-class              8.245  0.531   9.388
DynamicMarkerTable-class           8.335  0.417   9.151
GeneSetTable-class                 7.250  0.414   8.264
DynamicReducedDimensionPlot-class  7.216  0.316   7.944
registerFeatureSetCollections      6.054  0.381   7.068
modeGating                         5.425  0.262   6.081
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/iSEEu.Rcheck/00check.log’
for details.